6IFM Toxin Antitoxin Dna date Sep 20, 2018
title Crystal Structure Of Dna Bound Vapbc From Salmonella Typhimu
authors D.W.Park, B.J.Lee
compound source
Molecule: Trna(Fmet)-Specific Endonuclease Vapc
Chain: A, E, C, G
Synonym: Rnase Vapc,Toxin Vapc
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Salmonella Enterica Subsp. Enterica Se Typhimurium Str. Lt2;
Organism_taxid: 99287
Strain: Lt2 Sgsc1412 Atcc 700720
Gene: Vapc, Stm3033
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Antitoxin Vapb
Chain: B, F, H, D
Engineered: Yes

Organism_scientific: Salmonella Enterica Subsp. Enterica Se Typhimurium Str. Lt2;
Organism_taxid: 99287
Strain: Lt2 Sgsc1412 Atcc 700720
Gene: Vapb, Stm3034
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Forward (27-Mer)
Chain: M
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Backward (27-Mer)
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31
R_factor 0.206 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.677 93.677 122.440 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand
enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G
  • nuclease activity
  • endonuclease activity
  • ribonuclease activity


  • F, B, H, D


    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (6ifm.pdb1.gz) 151 Kb
  • CSU: Contacts of Structural Units for 6IFM
  • Structure Factors (1196 Kb)
  • Retrieve 6IFM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6IFM from S2C, [Save to disk]
  • View 6IFM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6IFM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ifm_N] [6ifm_C] [6ifm_M] [6ifm_E] [6ifm_D] [6ifm_H] [6ifm_A] [6ifm_B] [6ifm_F] [6ifm_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6IFM
  • Community annotation for 6IFM at PDBWiki (http://pdbwiki.org)

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